Membrane Packing Problems: A short Review on computational Membrane Modeling Methods and Tools

摘要

The use of model membranes is currently part of the daily workflow for many biochemical and biophysical disciplines. These membranes are used to analyze the behavior of small substances, to simulate transport processes, to study the structure of macromolecules or for illustrative purposes. But, how can these membrane structures be generated?This mini review discusses a number of ways to obtain these structures. First, the problem will be formulated as the Membrane Packing Problem. It will be shown that the theoretical problem of placing proteins and lipids onto a membrane area differ significantly. Thus, two sub-problems will be defined and discussed. Then, different – partly historical – membrane modeling methods will be introduced. And finally, membrane modeling tools will be evaluated which are able to semi-automatically generate these model membranes and thus, drastically accelerate and simplify the membrane generation process. The mini review concludes with advice about which tool is appropriate for which application case.